Analysis of age-associated genes and genomic regions
P-values are corrected for multiple testing using FDR. For each analysis, only the significant enrichment results (p < 0.01) are shown. Negative p-value indicates depletion. Tables show top 10 or less enriched/depleted associations, barplots visualize the same results. If an analysis does not have any significant results, it is not displayed at all.
Hannum meQTLs
Age-related meQTLs are non-cell type-specifically enriched in CTCF and depleted in Pol2.
## [1] "The total number of significantly ENRICHED associations is: 208"
##
## --------------------------------------------------------------------------------
## Row.names All.data V2
## ---------------------------------------- ---------- ----------------------------
## wgEncodeUwTfbsGm12874CtcfStdHotspotsRep2 7.14e-07 GM12874 CTCF TFBS ChIP-seq
## Hotspots 2 from ENCODE/UW
##
## wgEncodeSydhTfbsA549CtcfbIggrabPk 7.78e-07 A549 CTCF (SC-15914) IgG-rab
## ChIP-seq Peaks from
## ENCODE/SYDH
##
## wgEncodeUwTfbsA549CtcfStdHotspotsRep2 9.95e-07 A549 CTCF TFBS ChIP-seq
## Hotspots 2 from ENCODE/UW
##
## wgEncodeUwTfbsRptecCtcfStdHotspotsRep1 2.42e-06 RPTEC CTCF TFBS ChIP-seq
## Hotspots 1 from ENCODE/UW
##
## wgEncodeUwTfbsSaecCtcfStdHotspotsRep2 8.57e-06 SAEC CTCF TFBS ChIP-seq
## Hotspots 2 from ENCODE/UW
##
## wgEncodeUwTfbsHpafCtcfStdHotspotsRep2 2.73e-05 HPAF CTCF TFBS ChIP-seq
## Hotspots 2 from ENCODE/UW
##
## wgEncodeUwTfbsGm12864CtcfStdHotspotsRep1 2.73e-05 GM12864 CTCF TFBS ChIP-seq
## Hotspots 1 from ENCODE/UW
##
## wgEncodeUwTfbsAg10803CtcfStdHotspotsRep1 2.73e-05 AG10803 CTCF TFBS ChIP-seq
## Hotspots 1 from ENCODE/UW
##
## wgEncodeUwTfbsWi38CtcfStdHotspotsRep2 3.32e-05 WI-38 CTCF TFBS ChIP-seq
## Hotspots 2 from ENCODE/UW
##
## wgEncodeUwTfbsHrpeCtcfStdHotspotsRep2 3.32e-05 HRPEpIC CTCF TFBS ChIP-seq
## Hotspots 2 from ENCODE/UW
## --------------------------------------------------------------------------------
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly DEPLETED associations is: 34"
##
## -----------------------------------------------------------------------------------------
## Row.names All.data V2
## ------------------------------------------------ ---------- -----------------------------
## wgEncodeAwgTfbsBroadK562Phf8a301772aUniPk -8.34e-04 K562 TFBS Uniform Peaks of
## PHF8_(A301-772A) from
## ENCODE/Broad/Analysis
##
## wgEncodeAwgTfbsHaibA549Pol2Pcr2xDex100nmUniPk -9.16e-04 A549 (DEX_100nM) TFBS Uniform
## Peaks of Pol2 from
## ENCODE/HudsonAlpha/Analysis
##
## wgEncodeAwgTfbsHaibEcc1Pol2V0416102Dm002p1hUniPk -6.17e-04 ECC-1 (DMSO) TFBS Uniform
## Peaks of Pol2 from
## ENCODE/HudsonAlpha/Analysis
##
## wgEncodeAwgTfbsHaibH1hescTaf1V0416102UniPk -2.08e-03 H1-hESC TFBS Uniform Peaks of
## TAF1 from
## ENCODE/HudsonAlpha/Analysis
##
## wgEncodeAwgTfbsSydhGm12892Pol2IggmusUniPk -1.13e-03 GM12892 TFBS Uniform Peaks of
## Pol2 from
## ENCODE/Stanford/Analysis
##
## wgEncodeAwgTfbsSydhGm18951Pol2IggmusUniPk -4.52e-04 GM18951 TFBS Uniform Peaks of
## Pol2 from
## ENCODE/Stanford/Analysis
##
## wgEncodeHaibTfbsEcc1Pol2V0416102Dm002p1hPkRep1 -1.53e-03 ECC-1 Pol2 DMSO v041610.2
## ChIP-seq Peaks Rep 1 from
## ENCODE/HAIB
##
## wgEncodeHaibTfbsGm12878Taf1Pcr1xPkRep2 -2.80e-03 GM12878 TAF1 PCR1x ChIP-seq
## Peaks Rep 2 from ENCODE/HAIB
##
## wgEncodeHaibTfbsHelas3Pol2Pcr1xPkRep2 -1.45e-04 HeLa-S3 Pol2 PCR1x ChIP-seq
## Peaks Rep 2 from ENCODE/HAIB
##
## wgEncodeSydhTfbsHelas3Mxi1af4185IggrabPk -2.12e-03 HeLa-S3 Mxi1 IgG-rab ChIP-seq
## Peaks from ENCODE/SYDH
## -----------------------------------------------------------------------------------------
## [1] "---------------------------------------------------------------"Breast- and Kidney-specific age meQTL are enriched in NRSF transcription factor binding cites.
NRSF = RE1-Silencing Transcription factor (REST), also known as Neuron-Restrictive Silencer Factor (NRSF), is a protein which in humans is encoded by the REST gene, and acts as a transcriptional repressor.[1][2][3] REST is expressly involved in the repression of neural genes in non-neuronal cells.[4][3] Many genetic disorders have been tied to alterations in the REST expression pattern, including colon and small-cell lung carcinomas found with truncated versions of REST.[5] In addition to these cancers, defects in REST have also been attributed a role in Huntington Disease, neuroblastomas, and the effects of epileptic seizures and ischaemia. Interesting to note that REST strongly correlate with increased longevity. REST levels are highest in the brains of people who lived up to be 90 - 100s and remained cognitively intact.
## [1] "The total number of significantly ENRICHED associations is: 556"
##
## ---------------------------------------------------------------------------------------------------------------------
## Row.names pval.Breast pval.Kidney pval.Lung V2
## ----------------------------------------------- ------------- ------------- ----------- -----------------------------
## wgEncodeHaibTfbsU87NrsfPcr2xPkRep2V2 2.70e-02 4.89e-08 1.36e-02 U87 NRSF PCR2x ChIP-seq Peaks
## Rep 2 from ENCODE/HAIB
##
## wgEncodeHaibTfbsHepg2NrsfV0416101PkRep2 4.55e-02 1.19e-07 1.21e-02 HepG2 NRSF v041610.1 ChIP-seq
## Peaks Rep 2 from ENCODE/HAIB
##
## wgEncodeHaibTfbsSknshNrsfPcr2xPkRep2 2.70e-02 2.32e-07 1.36e-02 SK-N-SH NRSF PCR2x ChIP-seq
## Peaks Rep 2 from ENCODE/HAIB
##
## wgEncodeHaibTfbsA549Tead4sc101184V0422111PkRep1 2.70e-02 2.32e-07 1.36e-02 A549 TEAD4 v042211.1 ChIP-seq
## Peaks Rep 1 from ENCODE/HAIB
##
## wgEncodeHaibTfbsGm12878NrsfPcr2xPkRep1 2.70e-02 4.95e-07 1.36e-02 GM12878 NRSF PCR2x ChIP-seq
## Peaks Rep 1 from ENCODE/HAIB
##
## wgEncodeUwTfbsSknshraCtcfStdHotspotsRep1 6.59e-07 2.30e-02 6.54e-02 SK-N-SH_RA CTCF TFBS ChIP-seq
## Hotspots 1 from ENCODE/UW
##
## wgEncodeUwTfbsHepg2CtcfStdHotspotsRep1 9.59e-07 1.00e+00 3.08e-02 HepG2 CTCF TFBS ChIP-seq
## Hotspots 1 from ENCODE/UW
##
## wgEncodeUwTfbsHeeCtcfStdHotspotsRep1 1.24e-06 7.83e-01 6.22e-01 HEEpIC CTCF TFBS ChIP-seq
## Hotspots 1 from ENCODE/UW
##
## wgEncodeAwgTfbsUwGm12872CtcfUniPk 1.28e-06 6.48e-01 6.68e-02 GM12872 TFBS Uniform Peaks of
## CTCF from ENCODE/UW/Analysis
##
## wgEncodeAwgTfbsUwGm12875CtcfUniPk 1.28e-06 3.09e-01 2.80e-01 GM12875 TFBS Uniform Peaks of
## CTCF from ENCODE/UW/Analysis
## ---------------------------------------------------------------------------------------------------------------------
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly DEPLETED associations is: 1"
##
## -------------------------------------------------------------------------------------------------------
## Row.names pval.Breast pval.Kidney pval.Lung V2
## --------------------------------------- ------------- ------------- ----------- -----------------------
## wgEncodeSydhTfbsMcf10aesCmycTam14hHvdPk 7.90e-01 -8.33e-03 -3.09e-01 MCF10A c-Myc Harvard
## 4-hydroxytamoxifen 14hr
## ChIP-seq Peaks from
## ENCODE/SYDH
## -------------------------------------------------------------------------------------------------------
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly ENRICHED associations is: 63"
##
## --------------------------------------------------------
## Row.names pval.Breast pval.Kidney pval.Lung V2
## ----------- ------------- ------------- ----------- ----
## name.MAZ 1.47e-06 1.13e-01 5.30e-02
##
## name.RUNX3 7.97e-06 -2.24e-01 -5.41e-01
##
## name.FOXP2 1.07e-05 1.17e-01 3.57e-01
##
## name.BCLAF1 1.14e-05 4.65e-01 5.41e-01
##
## name.SIN3A 1.67e-05 5.62e-02 9.43e-02
##
## name.REST 5.03e-07 3.64e-05 5.30e-02
##
## name.ETS1 1.87e-05 7.69e-01 1.00e+00
##
## name.ELF1 1.96e-05 1.00e+00 1.90e-01
##
## name.PAX5 2.82e-05 -5.10e-01 1.00e+00
##
## name.CHD2 3.09e-05 2.63e-01 4.03e-01
## --------------------------------------------------------
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly ENRICHED associations is: 2"
##
## -------------------------------------------------------------------------------
## Row.names pval.Breast pval.Kidney pval.Lung V2
## ------------ ------------- ------------- ----------- --------------------------
## evoCpg 1.56e-02 2.19e-03 4.30e-01 Weizmann Evolutionary CpG
## Islands
##
## cpgIslandExt 1.44e-04 6.69e-08 7.99e-03 CpG Islands (Islands < 300
## Bases are Light Green)
## -------------------------------------------------------------------------------
## [1] "---------------------------------------------------------------"Hannum genes
Genes correlated with age are enriched in Pol2, EZH2-CTCF-RAD21-TAF2 complex. H3K27me3 Polycomb repressive complex 2 is recruited through the interaction of CTCF with Suz12, leading to allele-specific methylation at lysine 27 of histone H3
Enriched in GAD (genomic associations database), conserved. Depleted in genomeicSuperDups.
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly ENRICHED associations is: 6"
##
## --------------------------------
## Row.names mmc4_Genes_S6 V2
## ----------- --------------- ----
## POLR2A 9.44e-07
##
## EZH2 5.64e-06
##
## CTCF 9.86e-04
##
## RAD21 1.09e-03
##
## TAF1 1.13e-03
##
## ZNF263 3.04e-03
## --------------------------------
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly DEPLETED associations is: 10"
##
## --------------------------------
## Row.names mmc4_Genes_S6 V2
## ----------- --------------- ----
## ATF1 -1.06e-04
##
## BCLAF1 -1.98e-03
##
## ELK4 -3.50e-03
##
## IRF1 -5.70e-03
##
## KDM5A -2.09e-03
##
## MYBL2 -1.96e-03
##
## NR2C2 -6.96e-03
##
## RFX5 -3.87e-03
##
## SP4 -9.76e-03
##
## THAP1 -3.37e-03
## --------------------------------
## [1] "---------------------------------------------------------------"
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly ENRICHED associations is: 584"
##
## ----------------------------------------------------------------------------------------------------
## Row.names mmc4_Genes_S6 V2
## ------------------------------------------------------ --------------- -----------------------------
## wgEncodeUwHistoneMonocd14ro1746H3k27me3StdHotspotsRep1 1.17e-11 Monocytes-CD14+ RO 01746
## H3K27me3 Histone Mod ChIP-seq
## Hotspots 1 from ENCODE/UW
##
## wgEncodeUwHistoneGm12878H3k27me3StdHotspotsRep2 1.54e-11 GM12878 H3K27me3 Histone Mod
## ChIP-seq Hotspots 2 from
## ENCODE/UW
##
## wgEncodeUwHistoneH7esH3k27me3StdDiffa9dHotspotsRep1 4.45e-10 H7-hESC H3K27me3 diffProtA 9
## d Histone Mod ChIP-seq
## Hotspots 1 from ENCODE/UW
##
## wgEncodeSydhHistonePbmcH3k27me3bUcdPk 4.85e-10 PBMC H3K27me3 Histone
## Modifications by ChIP-Seq
## Peaks from ENCODE/SYDH
##
## wgEncodeUwHistoneH7esH3k27me3StdDiffa9dHotspotsRep2 1.25e-09 H7-hESC H3K27me3 diffProtA 9
## d Histone Mod ChIP-seq
## Hotspots 2 from ENCODE/UW
##
## wgEncodeUwHistoneGm06990H3k27me3StdHotspotsRep1 1.89e-09 GM06990 H3K27me3 Histone Mod
## ChIP-seq Hotspots 1 from
## ENCODE/UW
##
## wgEncodeUwHistoneH7esH3k27me3StdDiffa5dHotspotsRep2 2.78e-09 H7-hESC H3K27me3 diffProtA 5
## d Histone Mod ChIP-seq
## Hotspots 2 from ENCODE/UW
##
## wgEncodeUwHistoneH7esH3k27me3StdHotspotsRep2 6.22e-09 H7-hESC H3K27me3 Histone Mod
## ChIP-seq Hotspots 2 from
## ENCODE/UW
##
## wgEncodeUwHistoneMonocd14ro1746H3k27me3StdPkRep1 6.80e-09 Monocytes-CD14+ RO 01746
## H3K27me3 Histone Mod ChIP-seq
## Peaks 1 from ENCODE/UW
##
## wgEncodeUwHistoneH7esH3k27me3StdDiffa2dHotspotsRep1 7.78e-09 H7-hESC H3K27me3 diffProtA 2
## d Histone Mod ChIP-seq
## Hotspots 1 from ENCODE/UW
## ----------------------------------------------------------------------------------------------------
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly DEPLETED associations is: 226"
##
## ----------------------------------------------------------------------------------------------
## Row.names mmc4_Genes_S6 V2
## ------------------------------------------------ --------------- -----------------------------
## wgEncodeAwgTfbsHaibA549GabpV0422111Etoh02UniPk -1.22e-06 A549 (EtOH .02) TFBS Uniform
## Peaks of GABP from
## ENCODE/HudsonAlpha/Analysis
##
## wgEncodeAwgTfbsHaibGm12878Elf1sc631V0416101UniPk -1.07e-06 GM12878 TFBS Uniform Peaks of
## ELF1_(SC-631) from
## ENCODE/HudsonAlpha/Analysis
##
## wgEncodeAwgTfbsHaibK562Elf1sc631V0416102UniPk -1.49e-06 K562 TFBS Uniform Peaks of
## ELF1_(SC-631) from
## ENCODE/HudsonAlpha/Analysis
##
## wgEncodeHaibTfbsA549GabpV0422111Etoh02PkRep1 -9.69e-06 A549 GABP EtOH v042211.1
## ChIP-seq Peaks Rep 1 from
## ENCODE/HAIB
##
## wgEncodeHaibTfbsGm12878Elf1sc631V0416101PkRep1 -1.91e-06
##
## wgEncodeHaibTfbsGm12892Taf1V0416102PkRep1 -8.79e-06 GM12892 TAF1 v041610.2
## ChIP-seq Peaks Rep 1 from
## ENCODE/HAIB
##
## wgEncodeHaibTfbsHelas3GabpPcr1xPkRep2 -7.07e-06 HeLa-S3 GABP PCR1x ChIP-seq
## Peaks Rep 2 from ENCODE/HAIB
##
## wgEncodeHaibTfbsHepg2Hey1V0416101PkRep1 -1.40e-05
##
## wgEncodeHaibTfbsSknshraYy1sc281V0416102PkRep2 -6.33e-06 SK-N-SH RA YY1 281 v041610.2
## ChIP-seq Peaks Rep 2 from
## ENCODE/HAIB
##
## wgEncodeUwHistoneK562H3k04me3StdZnfa41c6PkRep1 -2.03e-06
## ----------------------------------------------------------------------------------------------
## [1] "---------------------------------------------------------------"
## [1] "---------------------------------------------------------------"
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly ENRICHED associations is: 3"
##
## --------------------------------------------------------------------------
## Row.names mmc4_Genes_S6 V2
## ------------------------------ --------------- ---------------------------
## gad 4.78e-07 Genetic Association Studies
## of Complex Diseases and
## Disorders
##
## phastConsElements46wayPrimates 7.77e-03 Primate Conserved Elements
##
## evoCpg 9.29e-03 Weizmann Evolutionary CpG
## Islands
## --------------------------------------------------------------------------
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly DEPLETED associations is: 1"
##
## -------------------------------------------------------------
## Row.names mmc4_Genes_S6 V2
## ---------------- --------------- ----------------------------
## genomicSuperDups -8.7e-06 Duplications of >1000 Bases
## of Non-RepeatMasked Sequence
## -------------------------------------------------------------
## [1] "---------------------------------------------------------------"
## [1] "---------------------------------------------------------------"
## [1] "---------------------------------------------------------------"
## [1] "---------------------------------------------------------------"Alisch
All enriched in H3K4me1. Methylated are enriched in H3K27me3 (reverse in demethylated). Demethylated are enriched in H3K4me1 (reverse in methylated). Methylated are enriched in EZH2, SUZ12 (reverse in demethylated, not significant in all).
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly ENRICHED associations is: 66"
##
## -------------------------------------------------------------------------------------------------------
## Row.names Alisch_et_al_Sup_Table2_all V2
## -------------------------------------------- ----------------------------- ----------------------------
## wgEncodeSydhHistonePbmcH3k4me1UcdPk 4.38e-32 PBMC H3K4me1 Histone
## Modifications by ChIP-Seq
## Peaks from ENCODE/SYDH
##
## wgEncodeBroadHistoneMonocd14ro1746H3k04me1Pk 5.46e-18 Monocytes CD14+ H3K4me1
## Histone Mods by ChIP-seq
## Peaks from ENCODE/Broad
##
## wgEncodeBroadHistoneGm12878H3k04me1StdPkV2 1.43e-13 GM12878 H3K4me1 Histone Mods
## by ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeBroadHistoneA549H3k04me1Etoh02Pk 2.15e-13 A549 EtOH 0.02% H3K4me1
## Histone Mods by ChIP-seq
## Peaks from ENCODE/Broad
##
## wgEncodeBroadHistoneHelas3H3k04me1StdPk 1.07e-12 HeLa-S3 H3K4me1 Histone Mods
## by ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeBroadHistoneA549H3k04me1Dex100nmPk 1.14e-12 A549 DEX 100 nM H3K4me1
## Histone Mods by ChIP-seq
## Peaks from ENCODE/Broad
##
## wgEncodeBroadHistoneNhekH3k4me1StdPk 3.81e-12 NHEK H3K4me1 Histone Mods by
## ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeBroadHistoneK562H3k4me1StdPk 1.08e-11 K562 H3K4me1 Histone Mods by
## ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeHaibMethyl450Nt2d1SitesRep1 3.71e-11 NT2-D1 Methylation 450K Bead
## Array from ENCODE/HAIB
##
## wgEncodeBroadHistoneGm12878H3k4me1StdPk 1.88e-12
## -------------------------------------------------------------------------------------------------------
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly DEPLETED associations is: 3147"
##
## ------------------------------------------------------------------------------------------------------------
## Row.names Alisch_et_al_Sup_Table2_all V2
## ------------------------------------------------ ----------------------------- -----------------------------
## wgEncodeAwgDnaseDukeGm12891UniPk -8.41e-49 GM12891 DNaseI HS Uniform
## Peaks from ENCODE/Analysis
##
## wgEncodeAwgDnaseDukeGm18507UniPk -3.54e-46 GM18507 DNaseI HS Uniform
## Peaks from ENCODE/Analysis
##
## wgEncodeAwgDnaseDukeGm19238UniPk -5.02e-46 GM19238 DNaseI HS Uniform
## Peaks from ENCODE/Analysis
##
## wgEncodeAwgDnaseUwCd34mobilizedUniPk -3.08e-53 CD34+_Mobilized DNaseI HS
## Uniform Peaks from
## ENCODE/Analysis
##
## wgEncodeHaibMethylRrbsEcc1HaibSitesRep2 -3.62e-52 ECC-1 Methyl-RRBS Rep 2 from
## ENCODE/HudsonAlpha
##
## wgEncodeHaibMethylRrbsT47dDm002p24hHaibSitesRep1 -1.37e-47 T-47D DMSO 0.02% 24 h
## Methyl-RRBS Rep 1 from
## ENCODE/HudsonAlpha
##
## wgEncodeUwDgfCd20ro01778Pk -2.70e-55 B cells CD20+ RO01778 DNaseI
## DGF Peaks from ENCODE/UW
##
## wgEncodeUwDgfGm06990Pk -1.78e-46 GM06990 DNaseI DGF Peaks from
## ENCODE/UW
##
## wgEncodeUwDnaseCd20ro01778PkRep1 -1.79e-50 B cells CD20+ RO01778 DNaseI
## HS Peaks Rep 1 from ENCODE/UW
##
## wgEncodeUwDnaseCd34mobilizedPkRep1 -2.78e-52 CD34+ Mobilized DNaseI HS
## Peaks Rep 1 from ENCODE/UW
## ------------------------------------------------------------------------------------------------------------
## [1] "---------------------------------------------------------------"
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly ENRICHED associations is: 232"
##
## ----------------------------------------------------------------------------------------------------------------------------------------------------------
## Row.names pval.Alisch_et_al_Sup_Table2_neg pval.Alisch_et_al_Sup_Table2_pos V2
## ------------------------------------------------------ ---------------------------------- ---------------------------------- -----------------------------
## wgEncodeUwHistoneMonocd14ro1746H3k27me3StdHotspotsRep1 -3.07e-04 1.42e-22 Monocytes-CD14+ RO 01746
## H3K27me3 Histone Mod ChIP-seq
## Hotspots 1 from ENCODE/UW
##
## wgEncodeBroadHistoneMonocd14ro1746H3k27me3Pk -1.90e-06 3.10e-22 Monocytes CD14+ H3K27me3
## Histone Mods by ChIP-seq
## Peaks from ENCODE/Broad
##
## wgEncodeUwHistoneHreH3k27me3StdHotspotsRep1 -6.92e-03 7.74e-20 HRE H3K27me3 Histone Mod
## ChIP-seq Hotspots 1 from
## ENCODE/UW
##
## wgEncodeUwHistoneH7esH3k27me3StdDiffa2dHotspotsRep1 -1.51e-02 2.05e-19 H7-hESC H3K27me3 diffProtA 2
## d Histone Mod ChIP-seq
## Hotspots 1 from ENCODE/UW
##
## wgEncodeBroadHistoneMonocd14ro1746H3k04me1Pk 6.92e-19 5.60e-01 Monocytes CD14+ H3K4me1
## Histone Mods by ChIP-seq
## Peaks from ENCODE/Broad
##
## wgEncodeUwHistoneH7esH3k27me3StdDiffa9dHotspotsRep2 -3.03e-02 1.87e-18 H7-hESC H3K27me3 diffProtA 9
## d Histone Mod ChIP-seq
## Hotspots 2 from ENCODE/UW
##
## wgEncodeBroadHistoneHelas3H3k04me1StdPk 2.66e-18 8.30e-01 HeLa-S3 H3K4me1 Histone Mods
## by ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeHaibMethyl450Nt2d1SitesRep1 3.94e-18 -6.03e-03 NT2-D1 Methylation 450K Bead
## Array from ENCODE/HAIB
##
## wgEncodeUwHistoneH7esH3k27me3StdDiffa9dHotspotsRep1 -9.06e-02 3.97e-18 H7-hESC H3K27me3 diffProtA 9
## d Histone Mod ChIP-seq
## Hotspots 1 from ENCODE/UW
##
## wgEncodeSydhHistonePbmcH3k27me3bUcdPk -9.07e-04 8.14e-18 PBMC H3K27me3 Histone
## Modifications by ChIP-Seq
## Peaks from ENCODE/SYDH
## ----------------------------------------------------------------------------------------------------------------------------------------------------------
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly DEPLETED associations is: 3358"
##
## ---------------------------------------------------------------------------------------------------------------------------------------------------------
## Row.names pval.Alisch_et_al_Sup_Table2_neg pval.Alisch_et_al_Sup_Table2_pos V2
## ----------------------------------------------------- ---------------------------------- ---------------------------------- -----------------------------
## wgEncodeAwgDnaseDukeIpsUniPk -1.19e-46 8.76e-01 iPS DNaseI HS Uniform Peaks
## from ENCODE/Analysis
##
## wgEncodeAwgDnaseUwdukeH1hescUniPk -8.87e-42 1.10e-01 H1-hESC DNaseI HS Uniform
## Peaks from ENCODE/Analysis
##
## wgEncodeHaibMethylRrbsAg04449UwSitesRep1 -3.89e-44 -1.33e-02 AG04449 Methyl-RRBS Rep 1
## from ENCODE/HudsonAlpha
##
## wgEncodeHaibMethylRrbsAg10803UwstamgrowprotSitesRep1 -2.10e-46 -1.28e-02
##
## wgEncodeHaibMethylRrbsBcliver0111002BiochainSitesRep1 -2.64e-42 -2.09e-02 Liver BC 01-11002 Methyl-RRBS
## Rep 1 from ENCODE/HudsonAlpha
##
## wgEncodeHaibMethylRrbsHipeUwstamgrowprotSitesRep1 -4.46e-42 -1.36e-01
##
## wgEncodeHaibMethylRrbsHnpceUwstamgrowprotSitesRep1 -9.49e-45 -1.94e-02
##
## wgEncodeHaibMethylRrbsHrpeUwSitesRep1 -4.62e-42 -5.69e-02 HRPEpiC Methyl-RRBS Rep 1
## from ENCODE/HudsonAlpha
##
## wgEncodeHaibMethylRrbsImr90UwSitesRep2 -1.30e-43 -1.27e-02
##
## wgEncodeHaibMethylRrbsPrecUwSitesRep1 -2.11e-44 -2.26e-02 PrEC Methyl-RRBS Rep 1 from
## ENCODE/HudsonAlpha
## ---------------------------------------------------------------------------------------------------------------------------------------------------------
## [1] "---------------------------------------------------------------"
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly ENRICHED associations is: 3"
##
## -------------------------------------------------------------------------------------------------------------------------
## Row.names pval.Alisch_et_al_Sup_Table2_neg pval.Alisch_et_al_Sup_Table2_pos pval.Alisch_et_al_Sup_Table2_all V2
## ----------- ---------------------------------- ---------------------------------- ---------------------------------- ----
## EZH2 -9.68e-09 1.65e-13 7.04e-01
##
## SUZ12 -8.44e-06 3.10e-05 -5.25e-01
##
## ESRRA 4.56e-03 -1.57e-01 8.72e-02
## -------------------------------------------------------------------------------------------------------------------------
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly DEPLETED associations is: 119"
##
## -------------------------------------------------------------------------------------------------------------------------
## Row.names pval.Alisch_et_al_Sup_Table2_neg pval.Alisch_et_al_Sup_Table2_pos pval.Alisch_et_al_Sup_Table2_all V2
## ----------- ---------------------------------- ---------------------------------- ---------------------------------- ----
## CHD1 -2.28e-12 -3.48e-01 -1.43e-10
##
## E2F6 -7.53e-16 -3.92e-02 -9.19e-16
##
## NFYB -2.73e-11 -1.10e-02 -5.93e-13
##
## RBBP5 -3.02e-19 -9.36e-01 -1.67e-13
##
## RELA -5.13e-13 -5.28e-02 -5.54e-14
##
## SIN3A -1.05e-13 -7.10e-02 -2.28e-14
##
## TAF7 -4.07e-17 -4.41e-02 -1.96e-17
##
## TCF3 -2.67e-13 -8.81e-01 -3.81e-11
##
## YY1 -2.65e-19 -1.40e-01 -6.15e-17
##
## ZBTB7A -1.04e-11 -8.49e-02 -2.16e-12
## -------------------------------------------------------------------------------------------------------------------------
## [1] "---------------------------------------------------------------"Rakyan
Hypermethylated regions are enriched in EZH2, H3K27me3.
## [1] "---------------------------------------------------------------"
## [1] "---------------------------------------------------------------"
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly ENRICHED associations is: 1"
##
## --------------------------------
## Row.names Supp_Table_3 V2
## ------------ -------------- ----
## varType.Gain 6.35e-03
## --------------------------------
## [1] "---------------------------------------------------------------"
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly ENRICHED associations is: 3"
##
## -------------------------------------------------------
## Row.names Supp_Table_3 V2
## ------------ -------------- ---------------------------
## cpgIslandExt 3.44e-07 CpG Islands (Islands < 300
## Bases are Light Green)
##
## evoCpg 3.32e-03 Weizmann Evolutionary CpG
## Islands
##
## gad 5.20e-03 Genetic Association Studies
## of Complex Diseases and
## Disorders
## -------------------------------------------------------
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly DEPLETED associations is: 1"
##
## ------------------------------------------------
## Row.names Supp_Table_3 V2
## ----------- -------------- ---------------------
## rmsk -1.35e-07 Repeating Elements by
## RepeatMasker
## ------------------------------------------------
## [1] "---------------------------------------------------------------"
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly ENRICHED associations is: 1"
##
## -------------------------------
## Row.names Supp_Table_3 V2
## ----------- -------------- ----
## name.EZH2 9.89e-10
## -------------------------------
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly DEPLETED associations is: 74"
##
## -------------------------------
## Row.names Supp_Table_3 V2
## ----------- -------------- ----
## name.CREB1 -1.64e-06
##
## name.E2F4 -1.64e-06
##
## name.ELF1 -6.27e-09
##
## name.JUND -1.49e-06
##
## name.MYC -2.38e-06
##
## name.PAX5 -1.98e-07
##
## name.PML -3.79e-08
##
## name.POU2F2 -2.72e-07
##
## name.RELA -1.73e-06
##
## name.RUNX3 -5.56e-06
## -------------------------------
## [1] "---------------------------------------------------------------"
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly ENRICHED associations is: 483"
##
## ---------------------------------------------------------------------------------------------------
## Row.names Supp_Table_3 V2
## ------------------------------------------------------ -------------- -----------------------------
## wgEncodeUwHistoneMonocd14ro1746H3k27me3StdHotspotsRep1 6.94e-18 Monocytes-CD14+ RO 01746
## H3K27me3 Histone Mod ChIP-seq
## Hotspots 1 from ENCODE/UW
##
## wgEncodeBroadHistoneMonocd14ro1746H3k27me3Pk 7.87e-18 Monocytes CD14+ H3K27me3
## Histone Mods by ChIP-seq
## Peaks from ENCODE/Broad
##
## wgEncodeUwHistoneH7esH3k27me3StdDiffa2dHotspotsRep1 5.28e-15 H7-hESC H3K27me3 diffProtA 2
## d Histone Mod ChIP-seq
## Hotspots 1 from ENCODE/UW
##
## wgEncodeBroadHistoneNhaEzh239875Pk 2.09e-14 NH-A EZH2 (39875) Histone
## Mods by ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeHaibMethyl450Helas3SitesRep1 2.10e-13 HeLa-S3 Methylation 450K Bead
## Array from ENCODE/HAIB
##
## wgEncodeUwHistoneH7esH3k27me3StdHotspotsRep1 1.82e-12 H7-hESC H3K27me3 Histone Mod
## ChIP-seq Hotspots 1 from
## ENCODE/UW
##
## wgEncodeUwHistoneHreH3k27me3StdHotspotsRep1 1.07e-11 HRE H3K27me3 Histone Mod
## ChIP-seq Hotspots 1 from
## ENCODE/UW
##
## wgEncodeUwHistoneH7esH3k27me3StdDiffa14dHotspotsRep1 1.21e-11 H7-hESC H3K27me3 diffProtA 14
## d Histone Mod ChIP-seq
## Hotspots 1 from ENCODE/UW
##
## wgEncodeBroadHistoneOsteoP300kat3bPk 2.84e-11 Osteoblasts P300 KAT3B
## Histone Mods by ChIP-seq
## Peaks from ENCODE/Broad
##
## wgEncodeHaibMethyl450JurkatSitesRep1 1.49e-11
## ---------------------------------------------------------------------------------------------------
## [1] "---------------------------------------------------------------"
## [1] "The total number of significantly DEPLETED associations is: 1360"
##
## --------------------------------------------------------------------------------------------
## Row.names Supp_Table_3 V2
## ----------------------------------------------- -------------- -----------------------------
## wgEncodeBroadHistoneDnd41H3k04me2Pk -1.17e-15 Dnd41 H3K4me2 Histone Mods by
## ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeBroadHistoneGm12878H3k04me3StdPkV2 -8.87e-15 GM12878 H3K4me3 Histone Mods
## by ChIP-seq Peaks from
## ENCODE/Broad
##
## wgEncodeBroadHistoneMonocd14ro1746H3k09acPk -1.80e-13 Monocytes CD14+ H3K9ac
## Histone Mods by ChIP-seq
## Peaks from ENCODE/Broad
##
## wgEncodeSydhTfbsRajiPol2UcdPk -9.59e-15 Raji Pol2 UC Davis ChIP-seq
## Peaks from ENCODE/SYDH
##
## wgEncodeUwDgfCd4naivewb11970640Hotspots -2.24e-14 CD4+ Naive Wb11970640 DNaseI
## DGF Hotspots from ENCODE/UW
##
## wgEncodeUwDnaseGm12864HotspotsRep1 -1.16e-13 GM12864 DNaseI HS HotSpots
## Rep 1 from ENCODE/UW
##
## wgEncodeUwDnaseGm12878HotspotsRep2 -8.41e-15 GM12878 DNaseI HS HotSpots
## Rep 2 from ENCODE/UW
##
## wgEncodeUwHistoneGm12864H3k04me3StdHotspotsRep1 -1.08e-15 GM12864 H3K4me3 Histone Mod
## ChIP-seq Hotspots 1 from
## ENCODE/UW
##
## wgEncodeUwHistoneGm12865H3k04me3StdHotspotsRep2 -5.41e-16 GM12865 H3K4me3 Histone Mod
## ChIP-seq Hotspots 2 from
## ENCODE/UW
##
## wgEncodeUwHistoneJurkatH3k4me3StdHotspotsRep1 -5.28e-14 Jurkat H3K4me3 Histone Mod
## ChIP-seq Hotspots 1 from
## ENCODE/UW
## --------------------------------------------------------------------------------------------
## [1] "---------------------------------------------------------------"